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Emre KARA avatar Ubuntu

Parallel Running Problem for PETSc

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Emre KARA

I have Ubuntu 20.04.3 LTS as a guest machine. I installed SU2 v7.2.1. I have no problem at serial running. I can parallel run some tutorials (for example with: mpirun -np 6 SU2_CFD example.cfg). However, I can serial run a tutorial (python3 /home/karae16/Documents/SU2-7.2.1/bin/fsi_computation.py -f fsi.cfg) but cannot parallel run it with the command given at the official website of SU2. Can anyone help me? The base memory is 7188/16384 MB. I installed PETSc with sudo. I don't remember if I use sudo or pip3 for Petsc4py The error I get is:

mpirun -np 6 python3 -m mpi4py /home/karae16/Documents/SU2-7.2.1/bin/fsi_computation.py --parallel -f fsi.cfg

[5]PETSC ERROR: ---------------------------------------------

[5]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range

[5]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger

[5]PETSC ERROR: or see https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind

[5]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors

[5]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run

[5]PETSC ERROR: to get more information on the crash.

[3]PETSC ERROR: ---------------------------------------------

[3]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range

[3]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger

[3]PETSC ERROR: or see https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind

[3]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors

[3]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run

[3]PETSC ERROR: to get more information on the crash.

[4]PETSC ERROR: ---------------------------------------------

[4]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range

[4]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger

[4]PETSC ERROR: or see https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind

[4]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors

[4]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run

[4]PETSC ERROR: to get more information on the crash.

[0]PETSC ERROR: ---------------------------------------------

[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range

[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger

[0]PETSC ERROR: or see https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind

[0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors

[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run

[0]PETSC ERROR: to get more information on the crash.

[1]PETSC ERROR: ---------------------------------------------

[1]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range

[1]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger

[1]PETSC ERROR: or see -

[1]PETSC ERROR: or try - on GNU/linux and Apple Mac OS X to find memory corruption errors

[1]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run

[1]PETSC ERROR: to get more information on the crash.

[2]PETSC ERROR: ---------------------------------------------

[2]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range

[2]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger

[2]PETSC ERROR: or see -

[2]PETSC ERROR: or try - on GNU/linux and Apple Mac OS X to find memory corruption errors

[2]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run

[2]PETSC ERROR: to get more information on the crash.

MPI_ABORT was invoked on rank 3 in communicator MPI_COMM_WORLD with errorcode 59.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them.

[karae16-VirtualBox:05661] 5 more processes have sent help message help-mpi-api.txt / mpi-abort [karae16-VirtualBox:05661] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages

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Victor Eijkhout avatar
cn flag
Victor Eijkhout
Your problem is not with parallelism, but with memory management. If you install a debug version of petsc you'll get better error reporting on where the segmentation fault happens.
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